FetalBrain - Gestational week associated analysis

Updated: Wed Dec 3 16:25:07 2014

DMR identification with methyl_diff

• Identify DM CpGs
  • methyl_diff one-sided p-value \(\le\) 0.005
    
  • delta fractional methylation \(\ge\) 0.5
    
  • fractional methylation of one sample \(\ge\) 0.75
    
• Collapse DM CpGs into DMRs
  • adjacent DM CpGs have the same DM status;
    
  • distance between adjacent CpGs (size) \(\le\) 300bp;
    
  • No. of CpGs within each DMR \(\ge\) 3.

Background

UMR summary and sanity check

• On average, there are 1692 17-week UMRs, 428 intersect between Cortex and GE, and 450 13-week UMRs, 76 intersect. The intersect is highly significant.
  
• Median DMR length is 321, comparable to breast. It’s similar in all chromosomes in 17-week UMRs, but fluctuate more in 13-week UMRs, probably due to small No. of UMRs identified.
  
• Median No. of CpGs per DMR is 5, also similar to breast.

Sample	Total.DMR	Hyper.DMR	Hypo.DMR
Cortex-HuFNSC02_Cortex-HuFNSC04	1283	179	1104
GE-HuFNSC02_GE-HuFNSC04	3002	722	2280

UMR asymmetry

• On average, there are , 4.8-fold enrichment in total UMR frequency in 17-week compared to 13-week, 8.17 in Cortex, and 3.97 in GE.

GREAT enrichment for GW-associated UMRs

• GREAT terms are strongly associated with neuron differentiation and brain development.
  
• 17-week UMRs are highly enriched in glial cell development in Cortex, and neural tube development in GE. Intersect of these two cell types show enrichment in cell fate commitment related to different types of brain cells.
  
• 13-week UMRs are enriched in neuron fate commitment in Cortex, and regionalization in GE. Intersect of these two cell types show no significant enrichment.

UMR Genomic breakdown

• On average, 62.26% of CpGs in UMRs overlap with genebody, and 23.95% of CpGs in UMRs overlap with promoters, 1.78-fold enriched. 44.87% of CpGs in UMRs overlap with CGIs, 5.97-fold than expected by random.

Proximal UMRs and DE genes

• On average, there are 165 UMRs proximally (TSS +/- 1.5kb) associated with protein-coding genes, 18.23% in 17-week UMRs, and 4.88% in 13-week UMRs, much lower than 17-week UMRs.
  
• Among proximal UMRs, 14.26% of 17-week proximal UMRs are associated with DE genes, 13.64% 13-week UMRs, similar to 17-week UMRs. On average, 20 DE genes are associated with GW UMRs.
  
• Among proximal UMR assocaited with DE genes, 79.55% 17-week UMRs change in the same direction as DE genes (hyper to DN), much higher than any Fetal Brain UMRs and close to observed in breast. 50% in 13-week UMRs, much lower than 17-week UMRs.

	proximal.DMRs	unique.genes	DE.DMRs	unique.DE.genes	same.direction
Cortex04.UMRs	7	7	0	0	0
Cortex02.UMRs	215	215	24	19	21
GE04.UMRs	37	36	6	5	3
GE02.UMRs	402	402	64	57	49

Proximal 13-week UMRs in both Cortex and GE

id	name	description
ENSG00000189334	S100A14	S100_calcium_binding_protein_A14_[Source:HGNC_Symbol;Acc:18901]
ENSG00000237693	IRGM	immunity-related_GTPase_family,M[Source:HGNC_Symbol;Acc:29597]
ENSG00000124564	SLC17A3	solute_carrier_family_17_(sodium_phosphate),member3_[Source:HGNC_Symbol;Acc:10931]

Proximal GE 13-week UMRs with DE genes

id	name	description	DM	DE
ENSG00000134954	ETS1	v-ets_erythroblastosis_virus_E26_oncogene_homolog_1_(avian)_[Source:HGNC_Symbol;Acc:3488]	hyper	UP
ENSG00000136352	NKX2-1	NK2_homeobox_1_[Source:HGNC_Symbol;Acc:11825]	hyper	UP
ENSG00000165588	OTX2	orthodenticle_homeobox_2_[Source:HGNC_Symbol;Acc:8522]	hyper	UP
ENSG00000231421			hyper	DN
ENSG00000155760	FZD7	frizzled_family_receptor_7_[Source:HGNC_Symbol;Acc:4045]	hyper	DN

Proximal 17-week UMRs with DE genes in both Cortex and GE

id	name	description	DM	DE
ENSG00000255737	NA	HCG2014417,isoformCRA_aUncharacterized_proteincDNA_FLJ59598_[Source:UniProtKB/TrEMBL;Acc:B7Z718]	hypo	UP
ENSG00000167178	ISLR2	immunoglobulin_superfamily_containing_leucine-rich_repeat_2_[Source:HGNC_Symbol;Acc:29286]	hypo	UP
ENSG00000161999	JMJD8	jumonji_domain_containing_8_[Source:HGNC_Symbol;Acc:14148]	hypo	UP
ENSG00000051523	CYBA	cytochrome_b-245,alphapolypeptide_[Source:HGNC_Symbol;Acc:2577]	hypo	UP
ENSG00000169515	CCDC8	coiled-coil_domain_containing_8_[Source:HGNC_Symbol;Acc:25367]	hypo	UP
ENSG00000205927	OLIG2	oligodendrocyte_lineage_transcription_factor_2_[Source:HGNC_Symbol;Acc:9398]	hypo	UP
ENSG00000189060	H1F0	H1_histone_family,member0_[Source:HGNC_Symbol;Acc:4714]	hypo	UP
ENSG00000146904	EPHA1	EPH_receptor_A1_[Source:HGNC_Symbol;Acc:3385]	hypo	UP
ENSG00000165072	MAMDC2	MAM_domain_containing_2_[Source:HGNC_Symbol;Acc:23673]	hypo	UP

UMRs overlapping with TFBS

TF	UMR17week_Cortex	UMR13week_Cortex	Ratio_Cortex	UMR17week_GE	UMR13week_GE	Ratio_GE
MAZ	133	5	26.6000	319	12	26.5833
GTF2F1	28	1	28.0000	103	2	51.5000
ZBTB7A	97	3	32.3333	201	3	67.0000
HMGN3	66	2	33.0000	131	4	32.7500
NRF1	34	1	34.0000	64	1	64.0000
MXI1	112	3	37.3333	262	7	37.4286
E2F4	50	1	50.0000	110	1	110.0000
CCNT2	87	1	87.0000	148	4	37.0000
E2F6	140	1	140.0000	263	8	32.8750

UMR enrichment at chromosome ends

DE genes summary

• On average, there are 754 genes differentially expressed between 13- and 17-week individuals, 254 up-regulated in 13-week individuals, and 499 up-regulated in 17-week individuals, 2-times as many.
  
• Within each cell type, majority of DE genes are shared among different comparisons (hypergeometric p-value = 0). There are 496 genes up-regulated in 17-week in cortex shared by at least two comparisons, 268 up-regulated in 13-week in cortex, 718 up-regulated in 17-week in GE, and 346 up-regulated in 13-week in GE.
  
• The overlap between cell types is highly significant as well (hypergeometric p-value = 0), with 270 genes up-regulated in 17-week in both cortex and GE supported by at least two comparisons, and 103 genes up-regulated in 13-week.

	UP	DN	DE
cortex01_cortex03	284	281	565
cortex01_cortex04	365	165	530
cortex02_cortex03	398	283	681
cortex02_cortex04	497	225	722
GE01_GE03	587	274	861
GE01_GE04	645	238	883
GE02_GE03	609	312	921
GE02_GE04	610	259	869

DAVID enrichment for DE genes

• Genes up-regulated in 17-week in both cortex and GE show enrichment in tissue development and calcium ion binding, they also show more brain development terms in GE.
  
• Genes up-regulated in 13-week in both cortex and GE show enrichment in neurogenesis.
  
• Genes shared by both cortex and GE show no significant terms, probably due to small No. of genes.
  

• In cortex:
  

• In GE:
  

Isoform analysis

• On average, there are 2153 isoform genes between 13- and 17-week individuals, majority of them are shared among different comparisons and between the two cell types (hypergeometric p-value = 0).
  
• There are 2878 isoform genes in cortex supported by at least two comparisons, and 2505 in GE, among them, 1800 isoform genes are shared between the two cell types.
  
• Isoform genes are enriched in cell signaling related terms.

	DE_genes	DE_exons	with_expressed_genes	isoform_exons	exclude_DE_genes	isoform_genes
cortex01_cortex03	565	28637	16045	8044	7772	2490
cortex01_cortex04	530	27428	13200	6365	6134	2167
cortex02_cortex03	681	28963	16765	7961	7630	2425
cortex02_cortex04	722	29416	13894	6351	6011	2105
GE01_GE03	861	31361	14725	5880	5458	2041
GE01_GE04	883	34359	15889	6401	5996	2049
GE02_GE03	921	32827	15557	5773	5306	1965
GE02_GE04	869	34699	16012	6113	5711	1986